[gmx-users] OPLS-AA atom types

[Justin A. Lemkul]

Austin B. Yongye wrote:
> Justin:
> I am using gromacs version 4.0.2. Several attempts to download current gromacs versions from http://www.gromacs.org/Downloads kept yielding 93.0-byte files. So I re-installed my pre-existing v4.0.2 without any problems (>./configure --enable-sse; make; make install).
> If you could send me the ffnonbonded.itp file that would be great.

You don't need it.  The corresponding file in 4.0.2 is called ffoplsaanb.itp. 
Newer Gromacs versions have a different directory and naming structure, but the 
contents of these files is the same.

Be aware that there have been dozens (if not hundreds) of usability upgrades, 
bug fixes, and new features that have been added since 4.0.2.  You would be 
well-served to try to figure out why you can't download a newer version.

-Justin

> Austin-
> 
> --- On Tue, 4/5/11, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> 
>> From: Justin A. Lemkul <jalemkul at vt.edu>
>> Subject: Re: [gmx-users] OPLS-AA atom types
>> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>> Date: Tuesday, April 5, 2011, 6:06 AM
>>
>>
>> Austin B. Yongye wrote:
>>> Thanks Justin.
>>> Could you/someone please forward the file? I don't
>> have it.
>>
>> It's part of your Gromacs installation. 
>> $GMXLIB/oplsaa.ff/ffnonbonded.itp.
>>
>> If you don't have it, then Gromacs wasn't properly
>> installed and you won't be 
>> able to use whatever force field for which you're designing
>> your topologies.
>>
>> -Justin
>>
>>> Austin-
>>>
>>> --- On Tue, 4/5/11, Justin A. Lemkul <jalemkul at vt.edu>
>> wrote:
>>>> From: Justin A. Lemkul <jalemkul at vt.edu>
>>>> Subject: Re: [gmx-users] OPLS-AA atom types
>>>> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>>>> Date: Tuesday, April 5, 2011, 5:19 AM
>>>>
>>>>
>>>> Austin B. Yongye wrote:
>>>>> Hello GROMACS USERS,
>>>>> Does any one have a document/manual/link that
>>>> describes the name-number atom type mappings
>> employed in
>>>> opls-aa?
>>>> The correspondence between the atom types and
>> bonded types
>>>> is all contained in ffnonbonded.itp.
>>>>
>>>> -Justin
>>>>
>>>>> I would like to build some molecules and
>> specify their
>>>> parameters, but I see different of numbers for the
>> same atom
>>>> type name, e.g:
>>>>> TYPE NAME
>>>>> 135  CT
>>>>> 136  CT
>>>>> 137  CT
>>>>> 157  CT
>>>>>
>>>>> I can deduce that 135 is CH3-, 136 is R-CH2-,
>> and 137
>>>> is RRCH- by looking at topology files.
>>>>> Thanks,
>>>>> Austin-
>>>> -- ========================================
>>>>
>>>> Justin A. Lemkul
>>>> Ph.D. Candidate
>>>> ICTAS Doctoral Scholar
>>>> MILES-IGERT Trainee
>>>> Department of Biochemistry
>>>> Virginia Tech
>>>> Blacksburg, VA
>>>> jalemkul[at]vt.edu | (540) 231-9080
>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>>
>>>> ========================================
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>> -- 
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================